On Sept. 5, JANA said in a Securities and Exchange Commission filing that its stake in energy company Oil States International had grown from 9.1 percent to 11.7 percent.

On Sept. 17, the hedge fund filed another government form, this time disclosing a 6.2 percent stake in supermarket chain Safeway (JANA said the company should cut stores in under-performing geographies; Safeway responded by closing Chicago-area Dominick's locations).

Barry Rosenstein's $7 billion firm is up 14.4 percent this year through September. The flagship hedge fund gained 3.2 percent last month alone on gains in three of its largest five positions: Oil States, Safeway and Japan Airlines.

"Stocks advanced in September in sympathy with the Fed taper being put on hold," the firm wrote in an update to investors obtained by CNBC.com. "Gross exposures are up slightly compared to the end of August, as we continue to populate the portfolio with compelling activist and value plus catalyst ideas."

JANA—which also gained 23.1 percent in 2012 after falling 2.1 percent in 2011—has increased its assets under management . The firm ran approximately $5.4 billion on Dec. 31 and $5.7 billion on July 1. As of Oct. 1, it's up to $7.02 billion.

The Absolute Return Event Driven Index, which tracks many activist hedge funds, is up 9.24 percent this year through September. It's the second-best performing strategy for 2013 after funds that specialize in distressed securities—they're up 9.31 percent on average.

Dan Loeb's Third Point Offshore is up 18.0 percent through September; Nelson Peltz's Trian Partners is up about 30 percent; and Jeffrey Ubben's ValueAct Capital Master Fund gained 19.8 percent, according to Alpha. Even relative laggards were positive for the year, including Paul Singer's Elliott Associates (up 9.3 percent) and Bill Ackman's Pershing Square International (up 0.2 percent).

Rick Teisch, director of research for North America at $2 billion fund of hedge funds Liongate Capital Management, said several factors have worked in the favor of activists this year,

"They tend to be significantly long-biased, which clearly benefits from such a strong tape. Mergers and acquisitions have been fairly healthy. Also, given the track record of activism and continuing changes to corporate governance, company managements have been far more receptive to working with hedge funds and other large shareholders like public pensions," Teisch said.

Investors are pleased with JANA's flexibility in what they invest in and for how long.

"The investments these days are not necessary terminal. They get in it and if they get a pop, they're gone," said a JANA client who asked to remain anonymous. "They're casting a much broader net—anywhere they can get management to do something and get the stock to go up."

JANA isn't done yet. On Thursday, Rosenstein said on CNBC that the firm would soon disclose another large stake in a company. He didn't say which one.